1,720,983 research outputs found
On the Extent of Linkage Disequilibrium in the Genome of Farm Animals
No full textGiven the importance of linkage disequilibrium (LD) in gene mapping and evolutionary inferences, I characterize in this review the pattern of LD and discuss the influence of human intervention during domestication, breed establishment, and subsequent genetic improvement on shaping the genome of livestock species. To this end, I summarize data on the profile of LD based on array genotypes vs. sequencing data in cattle and chicken, two major livestock species, and compare to the human case. This comparison provides insights into the real dimension of the pairwise allelic correlation and haplo-block structuring. The dependency of LD on allelic frequency is pictured and a recently introduced metric for moderating it is outlined. In the context of the contact farm animals had with human, the impact of genetic forces including admixture, mutation, recombination rate, selection, and effective population size on LD is discussed. The review further highlights the interplay of LD with runs of homozygosity and concludes with the operational implications of the widely used association and selection mapping studies in relation to LD
Mapping signatures of positive selection in the genome of livestock
No full textHuman driven selection during domestication and subsequent breed formation and breeding has left detectable signatures within the genome of livestock breeds. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology and for identifying selected genes that ultimately may help to further genetically improve these economically important species. Genome-wide screenings based on population techniques provide analytical tools to detect these signatures in relation to the act of selection. This review outlines a nonmathematical treatment of the theories and approaches available to scan the genome for evidence of positive selection and is intended for readers who are little or not familiar with population genetics theory. We discuss the genetics underlying phenotypic variation and adaptation and highlight molecular pattern that positive selection leaves behind along with the statistical approaches that are developed to detect such signatures. We describe some of the relative strengths and weaknesses of different strategies and also the challenges with identifying signatures of selection. Ascertainment bias with widely used SNP arrays is also a topic of interest. Finally we review approaches to assess the statistical significance of a signal at a particular locus or window and discuss factors affecting the statistical power to detect selective sweeps. (C) 2014 Published by Elsevier B.V
Data from: An evaluation of a novel estimator of linkage disequilibrium
No full textThe analysis of systems involving many loci is important in population and quantitative genetics. An important problem is the study of linkage disequilibrium (LD), a concept relevant in genome-enabled prediction of quantitative traits and in exploration of marker-phenotype associations. This article introduces a new estimator of a LD parameter (ρ^2) that is much easier to compute than a maximum likelihood (or Bayesian) estimate of a tetra-choric correlation. We examined the conjecture that the sampling distribution of the estimator of ρ^2 could be less frequency dependent than that of the estimator of r^2, a widely employed metric for assessing LD. This was done via an empirical evaluation of LD in 806 Holstein-Friesian cattle using 771 SNP markers, and of HapMap III data on 21,991 SNPs (chromosome 3) observed in 88 unrelated individuals from Tuscany. Also, 1600 haplotypes over a region of 1 Mb simulated under the coalescent were used to estimate LD using the two measures. Subsequently, a simulation study compared the new estimator with that of r2 using several scenarios of LD and allelic frequencies. From these studies it is concluded that ρ^2 provides a useful metric for the study of LD since the distribution of its estimator is less frequency-dependent than that of the standard estimator of r^2
A two-step method for detecting selection signatures using genetic markers
No full textSummaryA two-step procedure is presented for analysis of θ (FST) statistics obtained for a battery of loci, which eventually leads to a clustered structure of values. The first step uses a simple Bayesian model for drawing samples from posterior distributions of θ-parameters, but without constructing Markov chains. This step assigns a weakly informative prior to allelic frequencies and does not make any assumptions about evolutionary models. The second step regards samples from these posterior distributions as ‘data’ and fits a sequence of finite mixture models, with the aim of identifying clusters of θ-statistics. Hopefully, these would reflect different types of processes and would assist in interpreting results. Procedures are illustrated with hypothetical data, and with published allelic frequency data for type II diabetes in three human populations, and for 12 isozyme loci in 12 populations of the argan tree in Morocco.</jats:p
Assessing the degree of stratification between closely related Holstein-Friesian populations
No full textLinkage disequilibrium reveals different demographic history in egg laying chickens
Full text linkAbstract Background The availability of larger-scale SNP data sets in the chicken genome allows to achieve a higher resolution of the pattern of linkage disequilibrium (LD). In this study, 36 k and 57 k genotypes from two independent genotyping chips were used to systematically characterize genome-wide extent and structure of LD in the genome of four chicken populations. In total, we analyzed genotypes of 454 animals from two commercial and two experimental populations of white and brown layers which allows to some extent a generalization of the results. Results The number of usable SNPs in this study was 19 k to 37 k in brown layers and 8 k to 19 k in white layers. Our analyzes showed a large difference of LD between the lines of white and brown layers. A mean value of r2 = 0.73 ± 0.36 was observed in pair-wise distances of r2= 0.32 ± 0.33 was observed for SNPs less than 25 Kb apart from each other and dropped to 0.21 ± 0.26 at a distance of 100 kb in commercial brown layers. There was a remarkable similarity of the LD patterns among the two populations of white layers. The same was true for the two populations of brown layers, while the LD pattern between white and brown layers was clearly different. Inferring the population demographic history from LD data resulted in a larger effective population size in brown than white populations, reflecting less inbreeding among brown compared to white egg layers. Conclusions We report comprehensive LD map statistics for the genome of egg laying chickens with an up to 3 times higher resolution compared to the maps available so far. The results were found to be consistent between analyzes based on the parallel SNP chips and across different populations (commercial vs. experimental) within the brown and the white layers. It is concluded that the current density of usable markers in this study is sufficient for association mapping and the implementation of genomic selection in these populations to achieve a similar accuracy as in implementations of association mapping and genomic selection in mammalian farm animals.</p
Analysis of Relationship between Bovine Lymphocyte Antigen DRB3.2 Alleles, Somatic Cell Count and milk Traits in Iranian Holstein Population
No full textP>The major histocompatibility complex (MHC) is a gene complex closely linked to the vertebrate immune system due to its importance in antigen recognition and immune response to pathogens. To improve our understanding of the MHC and disease resistance in dairy cattle, we gathered 5119 test day records of somatic cell count (SCC) and performance traits of 262 Holstein dairy cows to determine whether the DRB region of the MHC contains alleles that are associated with elevated SCC, milk yield, protein and fat percent of milk. To this purpose, genotyping of animals for DRB3 gene was investigated by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) assay. A two-step PCR was carried out so as to amplify a 284 base-pair fragment of exon 2 of the target gene. Second PCR products were treated with three restriction endonuclease enzymes RsaI, BstYI and HaeIII. Twenty-eight BoLA-DRB3 alleles were identified including one novel allele ( 40). The results in general are in good accordance with allele frequencies of Holstein cattle populations reported by previous studies. Analyses of associations were modeled based on repeated measurement anova and generalized logistic linear methods for production traits and SCC data, respectively. The results of this study showed a significant relationship between the elevated SCC reflecting an increased probability of occurrence to subclinical mastitis and DRB3.2 allele 8 (p < 0.03). The results also revealed significant positive relationships of alleles 22 (p < 0.01) and allele 11 (p < 0.05) with milk fat percent as well as of alleles 24 (p < 0.03) and 22 (p < 0.05) with protein percent. The present study failed to find any association between milk yield and tested alleles. Because of the lack of consistency among results of similar studies, we suggest further investigations to determine the precise nature of these associations with the high polymorphic bovine MHC region to be performed based on haplotypes
DNA-based identification of novel bovine casein gene variants
No full textIn cattle, at least 39 variants of the 4 casein proteins (α(S1)-, β-, α(S2)- and κ-casein) have been described to date. Many of these variants are known to affect milk-production traits, cheese-processing properties, and the nutritive value of milk. They also provide valuable information for phylogenetic studies. So far, the majority of studies exploring the genetic variability of bovine caseins considered European taurine cattle breeds and were carried out at the protein level by electrophoretic techniques. This only allows the identification of variants that, due to amino acid exchanges, differ in their electric charge, molecular weight, or isoelectric point. In this study, the open reading frames of the casein genes CSN1S1, CSN2, CSN1S2, and CSN3 of 356 animals belonging to 14 taurine and 3 indicine cattle breeds were sequenced. With this approach, we identified 23 alleles, including 5 new DNA sequence variants, with a predicted effect on the protein sequence. The new variants were only found in indicine breeds and in one local Iranian breed, which has been phenotypically classified as a taurine breed. A multidimensional scaling approach based on available SNP chip data, however, revealed an admixture of taurine and indicine populations in this breed as well as in the local Iranian breed Golpayegani. Specific indicine casein alleles were also identified in a few European taurine breeds, indicating the introgression of indicine breeds into these populations. This study shows the existence of substantial undiscovered genetic variability of bovine casein loci, especially in indicine cattle breeds. The identification of new variants is a valuable tool for phylogenetic studies and investigations into the evolution of the milk protein genes
Properties of different selection signature statistics and a new strategy for combining them
No full textIdentifying signatures of recent or ongoing selection is of high relevance in livestock population genomics. From a statistical perspective, determining a proper testing procedure and combining various test statistics is challenging. On the basis of extensive simulations in this study, we discuss the statistical properties of eight different established selection signature statistics. In the considered scenario, we show that a reasonable power to detect selection signatures is achieved with high marker density (>1 SNP/kb) as obtained from sequencing, while rather small sample sizes (similar to 15 diploid individuals) appear to be sufficient. Most selection signature statistics such as composite likelihood ratio and cross population extended haplotype homozogysity have the highest power when fixation of the selected allele is reached, while integrated haplotype score has the highest power when selection is ongoing. We suggest a novel strategy, called de-correlated composite of multiple signals (DCMS) to combine different statistics for detecting selection signatures while accounting for the correlation between the different selection signature statistics. When examined with simulated data, DCMS consistently has a higher power than most of the single statistics and shows a reliable positional resolution. We illustrate the new statistic to the established selective sweep around the lactase gene in human HapMap data providing further evidence of the reliability of this new statistic. Then, we apply it to scan selection signatures in two chicken samples with diverse skin color. Our analysis suggests that a set of well-known genes such as BCO2, MC1R, ASIP and TYR were involved in the divergent selection for this trait
Parallel selection revealed by population sequencing in chicken.
No full textHuman driven selection during domestication and subsequent breed formation has likely left detectable signatures within the genome of modern chicken. The elucidation of these signatures of selection is of interest from the perspective of evolutionary biology, and for identifying genes relevant to domestication and improvement that ultimately may help to further genetically improve this economically important animal. We used whole genome sequence data from 50 hens of commercial white (WL) and brown (BL) egg laying chicken along with pool sequences of three meat type chicken to perform a systematic screening of past selection in modern chicken. Evidence of positive selection was investigated in two steps. First, we explored evidence of parallel fixation in regions with overlapping elevated allele frequencies in replicated populations of layers and broilers, suggestive of selection during domestication or pre-improvement ages. We confirmed parallel fixation in BCDO2 and TSHR genes and found four candidates including AGTR2, a gene heavily involved in 'Ascites' in commercial birds. Next, we explored differentiated loci between layers and broilers suggestive of selection during improvement of chicken. This analysis revealed evidence of parallel differentiation in genes relevant to appearance and production traits exemplified with the candidate gene OPG, implicated in Osteoporosis, a disorder related to over-consumption of calcium in egg laying hens. Our results illustrate the potential for population genetic techniques to identify genomic regions relevant to the phenotypes of importance to breeders
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